Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/03/3b4b0968f4a8e63f54d5c01886d93d/659_cX2_T1_TRNA_1_B2372Y3LT4_1.arriba.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d1/181ad5e24767ebd43981269bc2f774/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d1/181ad5e24767ebd43981269bc2f774/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/blacklist_breakpoint_database_2026-04-27.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/stage-fff52061-f714-4c14-bb2c-bf5549840817/43/06b80417dcdedb0d1513f19552f633/arriba_filter_config.yaml
==> STAGING COMPLETE (5 inputs)

  AIH curated blacklist: matched 9 fusion rows (breakpoint_ID in qualified set)

================================================================================
ARRIBA FILTERING SUMMARY
================================================================================

Total fusions: 875
  Pass (FILTER=PASS): 225 (25.7%)
  Fail (FILTER=FAIL): 650 (74.3%)

AIH curated blacklist (blacklisted flag):
  Total blacklisted: 9
  All 9 blacklisted rows have FILTER=FAIL

Failure reasons (top 15):
  confidence_below_min(medium<high): 163
  confidence_below_min(low<high);total_reads_below_min(1.0<8.0): 101
  confidence_below_min(medium<high);total_reads_below_min(3.0<8.0): 73
  confidence_below_min(medium<high);total_reads_below_min(4.0<8.0): 48
  confidence_below_min(medium<high);total_reads_below_min(5.0<8.0): 46
  confidence_below_min(medium<high);total_reads_below_min(2.0<8.0): 31
  confidence_below_min(low<high);total_reads_below_min(2.0<8.0): 30
  confidence_below_min(medium<high);total_reads_below_min(6.0<8.0): 25
  confidence_below_min(low<high);total_reads_below_min(3.0<8.0): 24
  confidence_below_min(medium<high);total_reads_below_min(7.0<8.0): 22
  total_reads_below_min(4.0<8.0): 14
  total_reads_below_min(6.0<8.0): 10
  total_reads_below_min(3.0<8.0): 9
  confidence_below_min(low<high);total_reads_below_min(0.0<8.0): 8
  total_reads_below_min(5.0<8.0): 8

Breakdown by confidence:
  high: 225 pass, 48 fail (total: 273)
  low: 0 pass, 187 fail (total: 187)
  medium: 0 pass, 415 fail (total: 415)
Arriba filter: 875 rows -> 225 PASS; wrote 659_cX2_T1_TRNA_1_B2372Y3LT4_1.arriba.fusions.filtered.tsv and 659_cX2_T1_TRNA_1_B2372Y3LT4_1.arriba.fusions.filtered_pass_only.tsv
Summary written to: 659_cX2_T1_TRNA_1_B2372Y3LT4_1.arriba.fusions.filter_summary.txt